├── LICENSE ├── README.md ├── graph-level ├── GT+HDSE │ ├── README.md │ ├── experiments │ │ ├── gt.sh │ │ ├── model_visu.py │ │ ├── sat.sh │ │ ├── train_SBMs.py │ │ ├── train_cifar.py │ │ ├── train_code2.py │ │ ├── train_ppa.py │ │ ├── train_zinc.py │ │ └── utils.py │ ├── s │ └── sat │ │ ├── __init__.py │ │ ├── coarsening_utils.py │ │ ├── data.py │ │ ├── gnn_layers.py │ │ ├── graph_utils.py │ │ ├── layers.py │ │ ├── maxWeightMatching.py │ │ ├── metric.py │ │ ├── models.py │ │ ├── position_encoding.py │ │ ├── spectral_clustering.py │ │ └── utils.py ├── GraphGPS+HDSE │ ├── README.md │ ├── configs │ │ └── GPS │ │ │ ├── cifar10-GPS-ESLapPE4.yaml │ │ │ ├── cluster-GPS-ESLapPE4.yaml │ │ │ ├── mnist-GPS-ESLapPE10.yaml │ │ │ ├── pattern-GPS-ESLapPE2.yaml │ │ │ ├── peptides-func-GPS3.yaml │ │ │ ├── peptides-struct-GPS10.yaml │ │ │ └── zinc-GPS+RWSE_3.yaml │ ├── graphgps │ │ ├── __init__.py │ │ ├── act │ │ │ ├── __init__.py │ │ │ └── example.py │ │ ├── config │ │ │ ├── __init__.py │ │ │ ├── custom_gnn_config.py │ │ │ ├── dataset_config.py │ │ │ ├── defaults_config.py │ │ │ ├── example.py │ │ │ ├── gt_config.py │ │ │ ├── optimizers_config.py │ │ │ ├── posenc_config.py │ │ │ ├── pretrained_config.py │ │ │ ├── split_config.py │ │ │ └── wandb_config.py │ │ ├── encoder │ │ │ ├── __init__.py │ │ │ ├── ast_encoder.py │ │ │ ├── composed_encoders.py │ │ │ ├── dummy_edge_encoder.py │ │ │ ├── equivstable_laplace_pos_encoder.py │ │ │ ├── example.py │ │ │ ├── kernel_pos_encoder.py │ │ │ ├── laplace_pos_encoder.py │ │ │ ├── linear_edge_encoder.py │ │ │ ├── linear_node_encoder.py │ │ │ ├── ppa_encoder.py │ │ │ ├── signnet_pos_encoder.py │ │ │ ├── type_dict_encoder.py │ │ │ └── voc_superpixels_encoder.py │ │ ├── finetuning.py │ │ ├── head │ │ │ ├── __init__.py │ │ │ ├── example.py │ │ │ ├── inductive_edge.py │ │ │ ├── inductive_node.py │ │ │ ├── ogb_code_graph.py │ │ │ └── san_graph.py │ │ ├── layer │ │ │ ├── __init__.py │ │ │ ├── bigbird_layer.py │ │ │ ├── example.py │ │ │ ├── gatedgcn_layer.py │ │ │ ├── gine_conv_layer.py │ │ │ ├── gps_layer.py │ │ │ ├── performer_layer.py │ │ │ ├── san2_layer.py │ │ │ └── san_layer.py │ │ ├── loader │ │ │ ├── __init__.py │ │ │ ├── dataset │ │ │ │ ├── __init__.py │ │ │ │ ├── __pycache__ │ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ │ ├── aqsol_molecules.cpython-39.pyc │ │ │ │ │ ├── coco_superpixels.cpython-39.pyc │ │ │ │ │ ├── malnet_tiny.cpython-39.pyc │ │ │ │ │ ├── peptides_functional.cpython-39.pyc │ │ │ │ │ ├── peptides_structural.cpython-39.pyc │ │ │ │ │ └── voc_superpixels.cpython-39.pyc │ │ │ │ ├── aqsol_molecules.py │ │ │ │ ├── coco_superpixels.py │ │ │ │ ├── malnet_tiny.py │ │ │ │ ├── pcqm4mv2_contact.py │ │ │ │ ├── peptides_functional.py │ │ │ │ ├── peptides_structural.py │ │ │ │ └── voc_superpixels.py │ │ │ ├── master_loader.py │ │ │ ├── ogbg_code2_utils.py │ │ │ └── split_generator.py │ │ ├── logger.py │ │ ├── loss │ │ │ ├── __init__.py │ │ │ ├── l1.py │ │ │ ├── multilabel_classification_loss.py │ │ │ ├── subtoken_prediction_loss.py │ │ │ └── weighted_cross_entropy.py │ │ ├── metric_wrapper.py │ │ ├── metrics_ogb.py │ │ ├── network │ │ │ ├── __init__.py │ │ │ ├── big_bird.py │ │ │ ├── custom_gnn.py │ │ │ ├── example.py │ │ │ ├── gps_model.py │ │ │ ├── performer.py │ │ │ └── san_transformer.py │ │ ├── optimizer │ │ │ ├── __init__.py │ │ │ └── extra_optimizers.py │ │ ├── pooling │ │ │ ├── __init__.py │ │ │ └── example.py │ │ ├── stage │ │ │ ├── __init__.py │ │ │ └── example.py │ │ ├── train │ │ │ ├── __init__.py │ │ │ ├── custom_train.py │ │ │ └── example.py │ │ ├── transform │ │ │ ├── __init__.py │ │ │ ├── coarsening_utils.py │ │ │ ├── graph_utils.py │ │ │ ├── maxWeightMatching.py │ │ │ ├── posenc_stats.py │ │ │ ├── spectral_clustering.py │ │ │ └── transforms.py │ │ └── utils.py │ ├── main.py │ ├── run │ │ ├── cancel_all.sh │ │ ├── run_experiments.sh │ │ └── wrapper.sb │ ├── setup.py │ ├── tests │ │ ├── configs │ │ │ ├── graph │ │ │ │ ├── cifar10.yaml │ │ │ │ ├── cluster-SAN.yaml │ │ │ │ ├── cluster.yaml │ │ │ │ ├── collab.yaml │ │ │ │ ├── dd.yaml │ │ │ │ ├── enzymes.yaml │ │ │ │ ├── imdb-binary.yaml │ │ │ │ ├── imdb-multi.yaml │ │ │ │ ├── malnettiny-GPS+RWSE.yaml │ │ │ │ ├── malnettiny-GPS-noPE.yaml │ │ │ │ ├── malnettiny-GPS.yaml │ │ │ │ ├── malnettiny-LapPE.yaml │ │ │ │ ├── malnettiny-SAN-sparse.yaml │ │ │ │ ├── malnettiny.yaml │ │ │ │ ├── mnist.yaml │ │ │ │ ├── nci1-LapPE.yaml │ │ │ │ ├── nci1-Performer.yaml │ │ │ │ ├── nci1.yaml │ │ │ │ ├── ogbg-code2-GPS.yaml │ │ │ │ ├── ogbg-code2.yaml │ │ │ │ ├── ogbg-molhiv-LapPE.yaml │ │ │ │ ├── ogbg-molhiv-RWSE.yaml │ │ │ │ ├── ogbg-molhiv-SAN+RWSE.yaml │ │ │ │ ├── ogbg-molhiv-SAN.yaml │ │ │ │ ├── ogbg-molhiv.yaml │ │ │ │ ├── ogbg-molpcba-GPS+RWSE-inference.yaml │ │ │ │ ├── ogbg-molpcba-GPS.yaml │ │ │ │ ├── ogbg-molpcba-LapPE.yaml │ │ │ │ ├── ogbg-molpcba-SAN.yaml │ │ │ │ ├── ogbg-molpcba.yaml │ │ │ │ ├── ogbg-ppa-GPS.yaml │ │ │ │ ├── ogbg-ppa.yaml │ │ │ │ ├── ogbl-collab.yaml │ │ │ │ ├── pattern-SAN.yaml │ │ │ │ ├── pattern.yaml │ │ │ │ ├── pcqm4m.yaml │ │ │ │ ├── proteins.yaml │ │ │ │ ├── zinc-BigBird.yaml │ │ │ │ ├── zinc-GPS+SignNet.yaml │ │ │ │ ├── zinc-GPS-BigBird.yaml │ │ │ │ ├── zinc-GPS-small.yaml │ │ │ │ ├── zinc-GPS.yaml │ │ │ │ ├── zinc-GPSwLPE.yaml │ │ │ │ ├── zinc-LapPE.yaml │ │ │ │ ├── zinc-Performer.yaml │ │ │ │ ├── zinc-SAN-LapPE+RWSE.yaml │ │ │ │ ├── zinc-SAN-small.yaml │ │ │ │ ├── zinc-SAN.yaml │ │ │ │ ├── zinc-SignNet.yaml │ │ │ │ └── zinc.yaml │ │ │ └── node │ │ │ │ ├── citeseer.yaml │ │ │ │ ├── cora.yaml │ │ │ │ ├── default.yaml │ │ │ │ ├── ogbn-arxiv.yaml │ │ │ │ └── pubmed.yaml │ │ ├── graph_run.sh │ │ ├── node_all_standard_split.sh │ │ └── node_run.sh │ └── unittests │ │ ├── __init__.py │ │ ├── test_eigvecs.py │ │ └── test_negate_edge_index.py └── README.md └── high-level-hdse ├── 100M ├── data_utils.py ├── dataset.py ├── load_data.py ├── load_graph.py ├── logger.py ├── metis_graph.py ├── nb-sample.py ├── ours.py ├── parse.py ├── run.sh └── vq.py ├── README.md ├── 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